100篇泛癌研究文献解读之泛癌拷贝数变异情况探索

关于SCNA

肿瘤的somatic的拷贝数变异，区别于肿瘤的somatic SNV，也非常重要，这里作者选取了11个癌症的近五千个样本，超过20万的CNA，平均每个样本是40个CNA,这里作者对SCNA进行分类：

• focal SCNAs that were shorter than the chromosome arm (median of 11 amplifications and 12 deletions per sample);
• arm-level SCNAs that were chromosome-arm length or longer (median of 3 amplifications and 5 deletions per sample);
• copy-neutral loss-of-heterozygosity (LOH) events in which one allele was deleted and the other was amplified coextensively (median of 1 per sample);
• whole-genome duplications (WGDs; in 37% of cancers).

肿瘤纯度和倍性的分布

很多软件都可以针对NGS数据计算肿瘤纯度和倍性，而且最新的TCGA pan-cancer计划，本来就会提供这些数据， https://gdc.cancer.gov/about-data/publications/panimmune

关于 Recurrent focal SCNAs

需要使用算法来得到显著的Recurrent focal SCNAs，比如GISTIC2算法

也有其它就，欢迎大家试用：RUBIC identifies driver genes by detecting recurrent DNA copy number breaks 有趣的是，发表到现在，引用才4个，Nat Commun. 2016 Jul

癌症特异性SCNAs

结论也平淡无奇，就是每个癌症内部都有SCNAs，是在泛癌分析结果里面没有的。

关于Chromothripsis

染色体破碎，Chromothripsis